The BOTTLE SHIP is surrounded by space dust, making the station look as if it is destroyed, and effectively adding to the abandoned/derelict atmosphere created by the ship.

The ship is later revealed to be a secret facility of the Galactic Federation containing many different lifeforms with the purpose of turning them into bioweapons, as well as breeding an army modelled after the Zebesian Pirate forces. The program is falsely indicated under Adam Malkovich's name. The facility eventually abandoned the Space Pirate-inspired army after the crew managed to breed a Queen Metroid and propagate Metroids in Sector Zero and interfaced with them via an A.I. in an android body named MB. The A.I is modelled after Mother Brain's and is able to communicate with Metroids through telepathy. However, at one point, MB went rampant and controlled the Space Pirate Forces to murder every Lab Worker except Madeline Bergman, the development director, who hid somewhere in the BOTTLE SHIP. The rogue android, claiming that all humans must be "judged", pilots the ship on an intercept course with the Galactic Federation as an attempt to attack and destroy it, but this plan was crushed completely when Samus and Adam intervened.

Shortly after Samus leaves, the Federation decides to destroy the BOTTLE SHIP. Samus returns to retrieve Adam's helmet, and escapes suitless from the exploding ship. When Samus first met MB (while she posed as Madeline Bergman), she had a vision of weapons being fired at the BOTTLE SHIP, creating a much more violent explosion than what is depicted in-game. Interestingly, this "vision" plays if Samus fails to escape in time.

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The BOTTLE SHIP likely refers to a Ship-in-a-bottle which consists of a model vessel assembled in a transparent glass bottle. This could be a reference to the feeling of entrapment or possibly to the mechanical puzzle aspect, in which the initial reaction to the object is a sense of confusion in regard to how the ship could have been placed into the bottle. These are commonly assembled, piece-by-piece, within the pre-made glass container. Or it might also refer to the ship's actual appearance, which is that of a sports or baby's bottle, where the "ringed" section represents the nozzle, and the larger section the container.

The BOTTLE SHIP being in the shape of a baby's bottle may also play into the theme of the baby's cry and possibly be a source of irony as the "Baby's Cry" distress signal came from within the baby's own bottle. Connecting to this theme, the BOTTLE SHIP houses MB, designed by the Federation to act as a nurturing mother figure toward the Metroids on board.

The BOTTLE SHIP contains many different species of creature and also quite a few mechanisms. While many are well known by Samus, there are many that are new to her as well. Most of the life forms were brought from Zebes, while others were found in previous planets visited by Samus, like Bryyo.

There are also several harmless species that are stored in the ship that serve no major role.

The BOTTLE SHIP bears a resemblance to the derelict G.F.S. Valhalla. The latter was also surrounded by similar-colored debris clouds.

The fact that the BOTTLE SHIP appears to be comprised of sectors mimicking various environments through holograms and seems to have been built to hold several species of creatures, make it seem very similar to the Biologic Space Laboratories research station in Other M's sequel, Metroid Fusion; the connection goes as far as all three sectors of the Bottle Ship and Sector Zero having a counterpart with a similar environment on the BSL. However, unlike the BSL, the BOTTLE SHIP's sectors are simulated and not real environments at all, and the BSL station, if they do in fact make bioweapons, at least attempt to hide that fact.

It seems some of these environments were created in the image of places Samus has been before. Their purpose is most likely to replicate the natural environment of the creatures (most of which have been previously encountered by Samus) and can thus survive naturally.

Anthony Higgs also mentions how onearea looks strangely similar to the Federation's training grounds. These said grounds on the BOTTLE SHIP could have been designed as an area to test the station's biological weapons.

The shape of the BOTTLE SHIP slightly resembles the design of Samus' Arm Cannon in the original Metroid.

In the Metroid: Other M Art Folio, there are areas referred to as "intentionally flooded." Some fans believed this referred to an aquatic sector ("Aquasphere" or "Hydrosphere"). In actuality, the encounter with Skulteras mentioned in this Folio takes place in the Biosphere.

All of the BOTTLE SHIP's doors are automatic. It shares this trait with Ceres.

Any time the name of the BOTTLE SHIP appears in the game's captions or the story option, it is written in all caps. The only other name to have this trait is the CONCENTRATION move when the Head Quarantine Officer asks Samus to use it at the beginning of the game, although it is spelled normally in the game's manual.

Text shown when looking at the terminal in the Exam Center seems to indicate that the BOTTLE SHIP explored in-game was one of three, before two of them had an unknown fate and the explored one was given to the Galactic Federation, however, some of the text is cut off by Maurice Favreau being in the way: "The terraforming capsule colony designated as BOTTLE SHIP is currently under the administration of the Galactic Federation. The ship supports animal specimens from various [text cut off] the purpose of biological-weapon research. There were originally two other BOTTLE SHIP, designed for use by interplanetary colonists by the Space Development Corporation. After long years of use, the first two ships were retired, and the remaining ship was given to the Galactic Federation. After extensive refitting, the ship was made able to sustain three distinct closed habitats, each designed to preserve various specimens collected from different planets for research and development in military-technology applications."[1]

"A distress signal known as a "Baby's Cry" drew me to this facility, which is listed as decommissioned. Its purpose is shrouded in mystery, although it's clear that its original design was to sustain and study life-forms in a variety of environments. Something has gone terribly wrong in this place."